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# Copyright 1999-2012 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
EAPI="4"
TEST_PV="4.0.4"
MANUAL_PV="4.5.4"
#to find external blas/lapack
CMAKE_MIN_VERSION="2.8.5-r2"
inherit bash-completion-r1 cmake-utils eutils fortran-2 multilib toolchain-funcs
SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )"
if [[ $PV = *9999* ]]; then
EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
https://gerrit.gromacs.org/gromacs.git
git://github.com/gromacs/gromacs.git
http://repo.or.cz/r/gromacs.git"
EGIT_BRANCH="release-4-6"
use hybrid && EGIT_BRANCH="nbnxn_hybrid_acc"
inherit git-2
else
SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz"
fi
ACCE_IUSE="fkernels power6 sse2 sse41 avx128fma avx256"
DESCRIPTION="The ultimate molecular dynamics simulation package"
HOMEPAGE="http://www.gromacs.org/"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
IUSE="X blas cuda doc -double-precision +fftw gsl hybrid lapack
mpi openmp +single-precision test +threads xml zsh-completion ${ACCE_IUSE}"
CDEPEND="
X? (
x11-libs/libX11
x11-libs/libSM
x11-libs/libICE
)
blas? ( virtual/blas )
cuda? ( dev-util/nvidia-cuda-toolkit )
fftw? ( sci-libs/fftw:3.0 )
fkernels? ( !threads? ( !altivec? ( !ia64? ( !sse2? ( virtual/fortran ) ) ) ) )
gsl? ( sci-libs/gsl )
lapack? ( virtual/lapack )
mpi? ( virtual/mpi )
xml? ( dev-libs/libxml2:2 )"
DEPEND="${CDEPEND}
dev-util/pkgconfig"
RDEPEND="${CDEPEND}
app-shells/tcsh"
RESTRICT="test"
REQUIRED_USE="cuda? ( !double-precision hybrid )"
pkg_pretend() {
[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
use openmp && ! tc-has-openmp && \
die "Please switch to an openmp compatible compiler"
if use cuda && [[ $(( $(gcc-major-version) * 10 + $(gcc-minor-version) )) -gt 44 ]] ; then
eerror "gcc 4.5 and up are not supported for useflag cuda!"
die "gcc 4.5 and up are not supported for useflag cuda!"
fi
}
pkg_setup() {
#notes/todos
# -on apple: there is framework support
# -mkl support
# -there are power6 kernels
if use fkernels; then
if use altivec || use ia64 || use sse2; then
ewarn "Gromacs only supports one acceleration method, in your case"
ewarn "the fortran kernel will be overwritten by (altivec|ia64|sse2)"
ewarn "so it is save to disable fkernels use flag!"
elif use threads; then
ewarn "Fortran kernels and threads do not work together, disabling"
ewarn "fortran kernels"
else
fortran-2_pkg_setup
fi
fi
}
src_prepare() {
#add user patches from /etc/portage/patches/sci-chemistry/gromacs
epatch_user
GMX_DIRS=""
use single-precision && GMX_DIRS+=" float"
use double-precision && GMX_DIRS+=" double"
#if neither single-precision nor double-precision is enabled
#build at least default (single)
[[ -z $GMX_DIRS ]] && GMX_DIRS+=" float"
for x in ${GMX_DIRS}; do
mkdir -p "${WORKDIR}/${P}_${x}" || die
use test && cp -r "${WORKDIR}"/gmxtest "${WORKDIR}/${P}_${x}"
done
}
src_configure() {
local mycmakeargs_pre=( )
#go from slowest to fastest acceleration
local acce="None"
use fkernels && use !threads && acce="Fortran"
use power6 && acce="Power6"
use sse2 && acce="SSE2"
use sse41 && acce="SSE4.1"
use avx128fma && acce="AVX_128_FMA"
use avx256 && acce="AVX_256"
#workaround for now
use sse2 && use hybrid && CFLAGS+=" -msse2"
mycmakeargs_pre+=(
-DGMX_FFT_LIBRARY=$(usex fftw fftw3 fftwpack)
$(cmake-utils_use X GMX_X11)
$(cmake-utils_use blas GMX_EXTERNAL_BLAS)
$(cmake-utils_use cuda GMX_GPU)
$(cmake-utils_use gsl GMX_GSL)
$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
$(cmake-utils_use openmp GMX_OPENMP)
$(cmake-utils_use xml GMX_XML)
-DGMX_DEFAULT_SUFFIX=off
-DGMX_ACCELERATION="$acce"
-DGMXLIB="$(get_libdir)"
-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
)
for x in ${GMX_DIRS}; do
einfo "Configuring for ${x} precision"
local suffix=""
#if we build single and double - double is suffixed
use double-precision && use single-precision && \
[[ ${x} = "double" ]] && suffix="_d"
local p
[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
$(cmake-utils_use threads GMX_THREAD_MPI)
-DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" )
CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
use mpi || continue
einfo "Configuring for ${x} precision with mpi"
mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_THREAD_MPI=OFF -DGMX_MPI=ON
-DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" )
CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
done
}
src_compile() {
for x in ${GMX_DIRS}; do
einfo "Compiling for ${x} precision"
CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}"\
cmake-utils_src_compile
use mpi || continue
einfo "Compiling for ${x} precision with mpi"
CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
cmake-utils_src_compile mdrun
done
}
src_test() {
for x in ${GMX_DIRS}; do
local oldpath="${PATH}"
export PATH="${WORKDIR}/${P}_${x}/src/kernel:${S}-{x}/src/tools:${PATH}"
cd "${WORKDIR}/${P}_${x}"
emake -j1 tests || die "${x} Precision test failed"
export PATH="${oldpath}"
done
}
src_install() {
for x in ${GMX_DIRS}; do
CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}" \
cmake-utils_src_install
use mpi || continue
#cmake-utils_src_install does not support args
#using cmake-utils_src_make instead
CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
cmake-utils_src_make install-mdrun DESTDIR="${D}"
done
rm -f "${ED}"/usr/bin/GMXRC*
newbashcomp "${ED}"/usr/bin/completion.bash ${PN}
if use zsh-completion ; then
insinto /usr/share/zsh/site-functions
newins "${ED}"/usr/bin/completion.zsh _${PN}
fi
rm -f "${ED}"/usr/bin/completion.*
# Fix typos in a couple of files.
sed -e "s:+0f:-f:" -i "${ED}"usr/share/gromacs/tutor/gmxdemo/demo \
|| die "Failed to fixup demo script."
cd "${S}"
dodoc AUTHORS INSTALL* README*
if use doc; then
newdoc "${DISTDIR}/gromacs-manual-${MANUAL_PV}.pdf" "manual-${MANUAL_PV}.pdf"
dohtml -r "${ED}usr/share/gromacs/html/"
fi
rm -rf "${ED}usr/share/gromacs/html/"
}
pkg_postinst() {
einfo
einfo "Please read and cite:"
einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
einfo "http://dx.doi.org/10.1021/ct700301q"
einfo
einfo $(g_luck)
einfo "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc"
einfo
elog "Gromacs can use sci-chemistry/vmd to read additional file formats"
if use hybrid; then
elog "Cuda and hybrid acceleration is still experimental,"
elog "use 'cutoff-scheme = Verlet' in your mdp file and"
elog "report bugs: http://redmine.gromacs.org/issues"
fi
}
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